CodeEntropy.FunctionCollection.EntropyFunctions.compute_entropy_residue_level¶
- CodeEntropy.FunctionCollection.EntropyFunctions.compute_entropy_residue_level(arg_hostDataContainer, arg_outFile=None, arg_selector='all', arg_moutFile=None, arg_nmdFile=None, arg_fScale=1.0, arg_tScale=1.0, arg_temper=300.0, arg_axis_list=['C', 'CA', 'N'], arg_verbose=3)[source]¶
Conpute the entropy at the residue level where each residue is treated as a separate bead for a
CodeEntropy.ClassCollection.DataContainer.DataContainer
system. Determining translation and rotation axes is part of the function. A common translation axes are used for all residues which is the principal axes of the whole molecule. The rotational axes are specific to each residue, which can be specified.- Parameters:
arg_hostDataContainer (CodeEntropy.ClassCollection.DataContainer.DataContainer) – Data Container for CodeEntropy
arg_outFile (str, optional, default: None) – Path to a output file output is written via append mode if it is not None.
arg_selector (str, optional, default: “all”) – Selection string for MDanalysis.Universe.select_atoms.
arg_moutFile (str, optional, default: None) – Print matrices if path to a matrices out file is not None.
arg_nmdFile (str, optional, default: None) – Print modespectra if path to a spectra out file is not None.
arg_fScale (float, optional, default: 1.0) – Force scale.
arg_tScale (float, optional, default: 1.0) – Torque scale.
arg_temper (float, optional, default: 300.0) – Temperature in K
arg_axis_list (list of str, optional, default: [‘C’, ‘CA’, ‘N’]) – The atom name of rotational axis of each residue. They must be present at each residue of selected atom system
arg_verbose (int, optional, default: 3) – Verbose level from 1-5
- Returns:
entropyFF (float) – Residue level level Force-Force Entropy in J/mol/K
entropyTT (float) – Residue level level Torque-Torque Entropy in J/mol/K